Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
24 hits were found for GGGGGAGGCACCUCAUUUU (5 guide strand hits and 19 sense strand hits.)
Hits to Guide strand
Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
NM_005777 | RBM6 | 574 | 592 | u | a | G | G | G | A | G | G | C | A | C | C | U | C | A | U | a | U | g | 58 | 4 | 14 | ac | false | <90% | 3639 | ||
XR_019652 | LOC392435 | 808 | 826 | G | G | a | G | G | A | G | G | C | A | C | u | U | C | A | U | U | U | U | 46 | 2 | 8 | false | <90% | 1145 | |||
XR_017125 | LOC392435 | 808 | 826 | G | G | a | G | G | A | G | G | C | A | C | u | U | C | A | U | U | U | U | 46 | 2 | 8 | false | <90% | 1145 | |||
NM_015691 | WWC3 | 5417 | 5435 | c | a | G | G | G | A | G | G | C | A | g | C | U | C | A | U | U | U | c | 20 | 4 | 8 | c | false | <90% | 6632 | ||
NM_016076 | C1orf121 | 1635 | 1653 | G | G | G | G | G | A | G | G | C | g | C | u | U | C | A | U | U | U | U | -16 | 2 | 9 | false | <90% | 4093 |
Hits to Sense strand
Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
NM_033641 | COL4A6 | 5834 | 5852 | g | A | A | A | U | G | A | G | G | U | G | C | C | a | C | C | C | a | g | 70 | 4 | 12 | c | false | <90% | 6689 | ||
NM_181833 | NF2 | 3543 | 3561 | A | u | A | c | U | G | A | G | G | U | G | C | C | U | C | C | C | C | a | 46 | 3 | 14 | bc | false | <90% | 4731 | ||
NM_181830 | NF2 | 4629 | 4647 | A | u | A | c | U | G | A | G | G | U | G | C | C | U | C | C | C | C | a | 46 | 3 | 14 | bc | false | <90% | 5817 | ||
NM_181828 | NF2 | 4752 | 4770 | A | u | A | c | U | G | A | G | G | U | G | C | C | U | C | C | C | C | a | 46 | 3 | 14 | bc | false | <90% | 5940 | ||
NM_181829 | NF2 | 4755 | 4773 | A | u | A | c | U | G | A | G | G | U | G | C | C | U | C | C | C | C | a | 46 | 3 | 14 | bc | false | <90% | 5943 | ||
NM_000268 | NF2 | 4833 | 4851 | A | u | A | c | U | G | A | G | G | U | G | C | C | U | C | C | C | C | a | 46 | 3 | 14 | bc | false | <90% | 6021 | ||
NM_016418 | NF2 | 4878 | 4896 | A | u | A | c | U | G | A | G | G | U | G | C | C | U | C | C | C | C | a | 46 | 3 | 14 | bc | false | <90% | 6066 | ||
NM_181832 | NF2 | 4893 | 4911 | A | u | A | c | U | G | A | G | G | U | G | C | C | U | C | C | C | C | a | 46 | 3 | 14 | bc | false | <90% | 6081 | ||
NM_032119 | GPR98 | 11880 | 11898 | c | c | u | A | U | G | A | G | G | U | G | C | C | U | C | C | a | C | C | 43 | 4 | 13 | c | false | <90% | 19333 | ||
NR_003149 | GPR98 | 11797 | 11815 | c | c | u | A | U | G | A | G | G | U | G | C | C | U | C | C | a | C | C | 43 | 4 | 13 | c | false | <90% | 19250 | ||
NM_203289 | POU5F1 | 875 | 893 | A | A | A | c | U | G | A | G | G | U | G | C | C | U | g | C | C | C | u | 33 | 3 | 10 | c | false | <90% | 1155 | ||
XR_016333 | LOC642559 | 1103 | 1121 | A | A | A | c | U | G | A | G | G | U | G | C | C | U | g | C | C | C | u | 33 | 3 | 10 | c | false | <90% | 1378 | ||
XR_019128 | LOC642559 | 1103 | 1121 | A | A | A | c | U | G | A | G | G | U | G | C | C | U | g | C | C | C | u | 33 | 3 | 10 | c | false | <90% | 1378 | ||
XR_017655 | LOC645682 | 1117 | 1135 | A | A | A | c | U | G | A | G | G | U | G | C | C | U | g | C | C | C | u | 33 | 3 | 10 | c | false | <90% | 1396 | ||
XR_019318 | LOC645682 | 1117 | 1135 | A | A | A | c | U | G | A | G | G | U | G | C | C | U | g | C | C | C | u | 33 | 3 | 10 | c | false | <90% | 1396 | ||
NM_002701 | POU5F1 | 1131 | 1149 | A | A | A | c | U | G | A | G | G | U | G | C | C | U | g | C | C | C | u | 33 | 3 | 10 | c | false | <90% | 1411 | ||
NM_018013 | SOBP | 3086 | 3104 | A | A | A | A | g | G | A | G | G | U | G | C | C | U | C | C | g | a | a | 17 | 4 | 11 | c | false | <90% | 6248 | ||
NM_017969 | IWS1 | 855 | 873 | A | A | A | A | U | G | A | G | G | a | G | C | C | U | C | C | C | a | a | 9 | 3 | 9 | c | false | <90% | 2950 | ||
NM_014567 | BCAR1 | 1353 | 1371 | u | g | u | A | U | G | c | G | G | U | G | C | C | U | C | C | C | C | C | 0 | 4 | 12 | bc | false | <90% | 3241 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2934
View matched accessions
3 prime seed match details
Immunostimulatory motif search results
UGUGU - Judge et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol. 2005 Apr;23(4):457-62. (PMID: 15778705)
No Immunostimulatory motif found (UGUGU).
GUCCUUCAA - Hornung et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med. 2005 Mar;11(3):263-70. Epub 2005 Feb 20. (PMID: 15723075)
No Immunostimulatory motif found (GUCCUUCAA).
Settings used for search
Scores were calculated using scoring scheme SS1
Using AVG scoring mode.
Hit scores
Parameter | Spec. Score cut-off | Colour | Comment |
Hit to same gene | Colour | Hits to the same accession or genes with 100 percent identity (i.e. likely transcript variants). It is advisable to always check the genes hit. | |
High scoring hit | ≥80 | Colour | Hits are very likely to cause an off-target effect |
Medium scoring hit | <80¸≥40 | Colour | Hits with a small chance of causing an off target effect. |
Low scoring hit | Colour | Hits very unlikely to cause an off-target effect |
The mismatches are colour coded based on the weighting of that position.
Cut-off | Colour |
Match | Colour |
Wobble base pairs (G-U) | Colour |
Critical bases (none) | Colour |
0.6 bits | Colour |
0.4 bits | Colour |
0.2 bits | Colour |
SpecificityServer is designed to help you identify potential non-specific matches to your siRNA. It incorporates the latest information about non-specific matches (sequence-specific only).
Designed by: Alistair Chalk, Quan Du, Zicai Liang and Erik L.L. Sonnhammer